Re: [gmx-users] soft-core and coulomb transformation

[David Mobley]

Berk,

> But what do you mean with charging and discharging?
>
> Going one way or the other in lambda does not matter.
> What matters is if there are particles that have zero charge
> in the A-state topology, while they have a non-zero charge
> in the B-state topology.

Sorry, what I mean by "charging" versus "discharging" is that
"charging" is where the A state has zero charges and the B state has
normal charges, and discharging is the reverse. So "charging" is the
scenario you describe, and "discharging" is the reverse.

David

> Berk.
>
>
> >From: "David Mobley" <[EMAIL PROTECTED]>
> >Reply-To: Discussion list for GROMACS users 
> >To: "bharat v. adkar" <[EMAIL PROTECTED]>
> >CC: Discussion list for GROMACS users 
> >Subject: Re: [gmx-users] soft-core and coulomb transformation
> >Date: Mon, 12 Nov 2007 10:26:37 -0800
> >
> >Following up on this issue, discharging phenol in water appears to
> >give the same results as charging phenol in water. In other words, so
> >far the only cases for which there seem to be a problem are relative
> >calculations (and so far I haven't looked at this for any other than
> >Bharat's test cases).
> >
> >Bharat, be sure you submit a bugzilla and we'll see how things go from
> >there. I may at some point try setting up some of my own relative free
> >energy topologies and see if I see the same effects, but I'm not
> >likely to have time for that for a couple days.
> >
> >Thanks,
> >David
> >
> >
> >
>
>
> _
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RE: [gmx-users] REMD As A Function of Distance Between 2 Chains

[Mu Yuguang (Dr)]

Dear Huey Ling,

In principle it is applicable. Then such REMD can be termed as
Hamiltonian REMD instead of canonical temperature REMD.

 

Dr. Yuguang Mu

School of Biological Sciences

60 Nanyang Drive 

Nanyang Technological Uiversity

Singapre

Tel: +65-63162885

email:ygmuATntu.edu.sg



From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Huey Ling Tan
Sent: Tuesday, November 13, 2007 2:24 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] REMD As A Function of Distance Between 2 Chains

 

Hi all,

Is it feasible to do parallel tempering (replica exchange) as a function
of distance with umbrella sampling applied?

I can do REMD for a system containing 2 peptide chains as a function as
temperatures, where I grompp each of the systems at different
temperatures, and then gather the fullmd.tpr files in one folder with
the script I want for full md run. 

But what if I want to do REMD as a function of distances (for example at
0.4, 0.6, 0.8, 1.0 nm between the chains, defined in the pull.ppa file),
at a fixed temperature, with umbrella sampling applied? If this can be
done, how should I write the script for the full md run so that each of
the pull.ppa files can recognise the system that it suppose to pull? 

If anyone know how this can be done?

Many thanks.

-- 
Best regards,
Huey Ling 

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[gmx-users] QMMM for element with "unknown" forcefield

[Tandia, Adama]

Dear GMX users,

I'm not very familiar with the QMMM implementation in Gromacs, but I
have two questions. 

1- I would like to run a MD simulation for glass materials that
contain B and Sb based oxides. Both elements are known to be multivalent
in the compositions that I'm interested. Is it possible to setup a QMMM
that assigns a sphere where QMMM is performed with a fixed radius around
Sb and B, and have the spheres to move with the assigned atoms during
the simulation? This would be a sort of Learn-On-The-Fly method.

2- Has anyone successfully compiled Gromacs 3.3.2 with QMMM set
to work with Gaussian or CPMD? If yes, can I request the details of the
compilation procedure?

Best wishes,

Adama

 
==
Adama Tandia
Modeling & Simulation
Corning INC
USA
 
Tel:  607 248 1036
Fax: 607 974 3405
www.corning.com

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Re: [Bulk] Re: [gmx-users] force=nan in frame 0

[Yang Ye]

You can send me the file off the list. To solve this kind of problem, 
start from simple case: two or a handful of atoms.


Regards,
Yang Ye

On 11/13/2007 5:36 AM, Dongsheng Zhang wrote:

Dear Yang Ye,

Thank you very much for your reply. You are very helpful in my 
experience. I turned off the nb interaction
by c6=0, c12 = 0. If you need my force field, I can give you the 
package for testing.


All the best!

Dongsheng

- Original Message 
From: Yang Ye <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users 
Sent: Monday, November 12, 2007 2:33:38 PM
Subject: Re: [gmx-users] force=nan in frame 0

how do you turn off the interactions? e.g. setting rvdw=0 doesn't mean
turning of vdw interactions.

Regards,
Yang Ye

On 11/13/2007 12:55 AM, dongsheng zhang wrote:
> Dear Mark,
>
> The installation works for other systems. The error happens in 
either EM or

> MD. When I turn off all interaction potentials, the forces between all
> particles should be zero, shouldn't they? Could you please tell me 
why the

> initial forces are NaN? Thanks!
>
> All the best!
>
> Dongsheng
>
> -Original Message-
> From: [EMAIL PROTECTED] 
 
[mailto:[EMAIL PROTECTED] 
]

> On Behalf Of Mark Abraham
> Sent: Sunday, November 11, 2007 9:04 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] force=nan in frame 0
>
>
> dongsheng zhang wrote:
> 
>> Dear Mark,

>>
>> Thank you for your reply. I have used gromacs before. In fact, I have
>> built this FF before, and using it successfully. My old computer was
>> crashed, so I need to do it again. The potential energies looked fine
>> in the md.log. Even I turn off all potentials. I still get the initial
>> foce = nan. Could you please give me any suggest about it?
>>   
>
> Can't tell. You still haven't told us what you were trying to do 
when it

> crashed. EM, MD? Did you minimize and/or equilibrate? Does this
> installation run other systems?
>
> Mark
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Re: [gmx-users] force=nan in frame 0

[Dongsheng Zhang]

Dear Yang Ye,

Thank you very much for your reply. You are very helpful in my experience. I 
turned off the nb interaction
by c6=0, c12 = 0. If you need my force field, I can give you the package for 
testing.

All the best!

Dongsheng

- Original Message 
From: Yang Ye <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users 
Sent: Monday, November 12, 2007 2:33:38 PM
Subject: Re: [gmx-users] force=nan in frame 0


how do you turn off the interactions? e.g. setting rvdw=0 doesn't mean 
turning of vdw interactions.

Regards,
Yang Ye

On 11/13/2007 12:55 AM, dongsheng zhang wrote:
> Dear Mark,
>
> The installation works for other systems. The error happens in either
 EM or
> MD. When I turn off all interaction potentials, the forces between
 all
> particles should be zero, shouldn't they? Could you please tell me
 why the
> initial forces are NaN? Thanks!
>
> All the best!
>
> Dongsheng
>
> -Original Message-
> From: [EMAIL PROTECTED]
 [mailto:[EMAIL PROTECTED]
> On Behalf Of Mark Abraham
> Sent: Sunday, November 11, 2007 9:04 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] force=nan in frame 0
>
>
> dongsheng zhang wrote:
>   
>> Dear Mark,
>>
>> Thank you for your reply. I have used gromacs before. In fact, I
 have 
>> built this FF before, and using it successfully. My old computer was
 
>> crashed, so I need to do it again. The potential energies looked
 fine 
>> in the md.log. Even I turn off all potentials. I still get the
 initial 
>> foce = nan. Could you please give me any suggest about it?
>> 
>
> Can't tell. You still haven't told us what you were trying to do when
 it 
> crashed. EM, MD? Did you minimize and/or equilibrate? Does this 
> installation run other systems?
>
> Mark
> ___
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 posting!
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 post? Read
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 posting!
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>   

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Re: [gmx-users] soft-core and coulomb transformation

[Berk Hess]

Hi,

But what do you mean with charging and discharging?

Going one way or the other in lambda does not matter.
What matters is if there are particles that have zero charge
in the A-state topology, while they have a non-zero charge
in the B-state topology.

Berk.



From: "David Mobley" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users 
To: "bharat v. adkar" <[EMAIL PROTECTED]>
CC: Discussion list for GROMACS users 
Subject: Re: [gmx-users] soft-core and coulomb transformation
Date: Mon, 12 Nov 2007 10:26:37 -0800

Following up on this issue, discharging phenol in water appears to
give the same results as charging phenol in water. In other words, so
far the only cases for which there seem to be a problem are relative
calculations (and so far I haven't looked at this for any other than
Bharat's test cases).

Bharat, be sure you submit a bugzilla and we'll see how things go from
there. I may at some point try setting up some of my own relative free
energy topologies and see if I see the same effects, but I'm not
likely to have time for that for a couple days.

Thanks,
David





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Re: [gmx-users] force=nan in frame 0

[Yang Ye]

how do you turn off the interactions? e.g. setting rvdw=0 doesn't mean 
turning of vdw interactions.


Regards,
Yang Ye

On 11/13/2007 12:55 AM, dongsheng zhang wrote:

Dear Mark,

The installation works for other systems. The error happens in either EM or
MD. When I turn off all interaction potentials, the forces between all
particles should be zero, shouldn't they? Could you please tell me why the
initial forces are NaN? Thanks!

All the best!

Dongsheng

-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Mark Abraham
Sent: Sunday, November 11, 2007 9:04 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] force=nan in frame 0


dongsheng zhang wrote:
  

Dear Mark,

Thank you for your reply. I have used gromacs before. In fact, I have 
built this FF before, and using it successfully. My old computer was 
crashed, so I need to do it again. The potential energies looked fine 
in the md.log. Even I turn off all potentials. I still get the initial 
foce = nan. Could you please give me any suggest about it?



Can't tell. You still haven't told us what you were trying to do when it 
crashed. EM, MD? Did you minimize and/or equilibrate? Does this 
installation run other systems?


Mark
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Re: [gmx-users] trjorder does not write trajectory file

[Dmytro Kovalskyy]

> Dmytro Kovalskyy wrote:
>>> It works fine for me under 3.3.1 - what command line are you issuing?
>> trjorder -f traj.xtc -s topol.tpr -o 5A -nshell 5A -r 0.5
Thanks, this work for me. However, It is not obvious from the help. An
output trajectory is not defined as Option and i supposed it is written
always.
I think this should be reflected in help page.

Dima
>
> Reading the source, both -nshell and -r enforce no trajectory output.
>
> Mark
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> !DSPAM:47370f07297651661515522!
>
>


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Re: [gmx-users] soft-core and coulomb transformation

[David Mobley]

Following up on this issue, discharging phenol in water appears to
give the same results as charging phenol in water. In other words, so
far the only cases for which there seem to be a problem are relative
calculations (and so far I haven't looked at this for any other than
Bharat's test cases).

Bharat, be sure you submit a bugzilla and we'll see how things go from
there. I may at some point try setting up some of my own relative free
energy topologies and see if I see the same effects, but I'm not
likely to have time for that for a couple days.

Thanks,
David


On 11/12/07, David Mobley <[EMAIL PROTECTED]> wrote:
> Hi, Bharat, and David vdS.
>
> This indeed is looking suspiciously like a real problem. FWIW, I did
> reproduce your original problem using my own input files and PME with
> gromacs 3.3.1.
>
> It's still a bit perplexing, in that you seem to be getting basically
> the "right" answers for the forward transformation (at least, by
> comparing the PME forward results with the cutoff forward results) but
> the reverse transformation is crazily wrong. I'm having a hard time
> figuring out what sort of bug could cause this to happen.
>
> The only thing I can come up with so far that might cause this is a
> bug in the handling of B state 1-4 interactions with PME. Since
> methane has no B state 1-4 electrostatic interactions, the
> ethane->methane transformation would be OK both with and without PME.
> But methane->ethane would go awry with PME because ethane still has
> 1-4 electrostatic interactions.
>
> If I remember correctly, though, you reported that the vacuum
> calculations work fine? That wouldn't be consistent with my
> explanation above, and perhaps would suggest that the problem is
> interactions with water, somehow?
>
> Just speculation at this point.
>
> I'm doing some more testing on this end (trying to come up with a more
> minimal example). I'm checking to see whether discharging phenol in
> water gives the same results as charging phenol in water.
>
> David
>
>
> On 11/11/07, bharat v. adkar <[EMAIL PROTECTED]> wrote:
> >
> > Hi David,
> >I am keeping the subject same so that it is helpful to track in
> > future :)
> >
> >
> > On Sat, 10 Nov 2007, David Mobley wrote:
> > > Dear Bharat,
> > >
> > > OK, I went ahead and ran with your topologies using my own run
> > > scripts. My runs haven't finished yet,  but looking at just
> > >  values from equilibration,  I seem to be seeing roughly
> > > the same trends you do. In particular:
> > > (1) The forward simulation always gives dv/dlambda values that are
> > > fairly close to -2 at each lambda
> > > (2) The reverse simulation gives a range of  values at
> > > different lambda values, and switches from positive to negative as
> > > lambda increases.
> > >
> > > The integral of  in the forward case is NOT the negative
> > > of the integral of  for the reverse case, which is what it
> > > should be.
> > >
> > > Obviously, something is wrong here, and it doesn't seem to be your run
> > > input files. I don't see anything obviously wrong with your topology
> > > files, either -- as far as I can tell your charge groups are OK.
> > >
> > > My suggestion is to try to strip this down to a simpler case where it
> > > will become more clear what the problem is. Maybe ethane->methane
> > > rather than with the capping on the ends.  (Did you say you have the
> > > same problem with ethane->methane? It would be easier to troubleshoot
> > > those topologies).
> >
> > As I mentioned earlier, ethane to methane transformation also shows the
> > same behaviour. I am almost sure that the topologies and other input
> > files are correct. I am pasting below the output of the
> > coulomb-transformation for both, ethane to methane (forward) and methane
> > to ethane (reverse). Topology is the same as i mentioned few mails
> > back...
> >
> > Forward charge transformation
> > lmbd  dg/dlerror
> > 0.00 -8.286304 0.0108319
> > 0.05 -8.32708  0.0114018
> > 0.10 -8.328157 0.0095819
> > 0.15 -8.344236 0.00893341
> > 0.25 -8.353463 0.00984712
> > 0.40 -8.368163 0.0104302
> > 0.50 -8.397035 0.00969758
> > 0.60 -8.415603 0.00908416
> > 0.75 -8.448185 0.00941215
> > 0.85 -8.484247 0.00922024
> > 0.90 -8.481465 0.00885981
> > 0.95 -8.495802 0.00961897
> > 1.00 -8.501283 0.00957299
> >
> > Reverse charge transformation
> > 0.00 13.770658 0.074592
> > 0.05 13.331217 0.0778554
> > 0.10 13.075527 0.0722786
> > 0.15 12.483814 0.0750718
> > 0.25 11.789282 0.0674654
> > 0.40 10.730386 0.0875609
> > 0.50 10.008684 0.0807128
> > 0.60  9.266026 0.0736956
> > 0.75  7.999017 0.0738001
> > 0.85  7.388243 0.0832792
> > 0.90  6.991334 0.0828869
> > 0.95  6.595921 0.0796503
> > 1.00  6.180366 0.0893983
> >
> > As can be clearly seen, both transformations are not equivalent. (These
> > are output from the 1 ns simulations.)
> >
> >
> > >
> > > If you get to the point where you're convinced it has nothing to do
> > > with your topology, you could submit a bugzilla -- but it wo

[gmx-users] REMD As A Function of Distance Between 2 Chains

[Huey Ling Tan]

Hi all,

Is it feasible to do parallel tempering (replica exchange) as a function of
distance with umbrella sampling applied?

I can do REMD for a system containing 2 peptide chains as a function as
temperatures, where I grompp each of the systems at different temperatures,
and then gather the fullmd.tpr files in one folder with the script I want
for full md run.

But what if I want to do REMD as a function of distances (for example at 0.4,
0.6, 0.8, 1.0 nm between the chains, defined in the pull.ppa file), at a
fixed temperature, with umbrella sampling applied? If this can be done, how
should I write the script for the full md run so that each of the
pull.ppafiles can recognise the system that it suppose to pull?

If anyone know how this can be done?

Many thanks.

-- 
Best regards,
Huey Ling
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RE: [gmx-users] mdrun error

[pragya chohan]

hi 
i tried to run the simulation with single alamethicin molecule but i am getting 
the same error as i was getting earlier.
Warning: 1-4 interaction between 164 and>> 169 at distance 3.430 which is 
larger than the 1-4 table size 1.000 nm.
I used the command 
 $ genbox -cp alamethicin.gro -cs popc.gro -o system.gro 
my pdb file at 164 to 169 is:
ATOM 164 CZ PHL 21 44.000 52.840 35.170 1.00 0.00
ATOM 165 HZ PHL 21 44.990 53.260 35.090 1.00 0.00
ATOM 166 CX PHL 21 38.140 50.450 37.160 1.00 0.00
ATOM 167 OY PHL 21 37.940 49.350 38.060 1.00 0.00
ATOM 168 HY PHL 21 37.040 48.940 37.950 1.00 0.00
ATOM 169 CA ACE 22 53.840 44.410 66.930 1.00 0.00.
This is occuring at the start of equillibration step . I have not done any 
simulation as yet. 
I also tried pre-equillibrating the protein and directly simulating by restrain 
but that also is not working.

I cannot figure out the problem. Please help

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Re: [gmx-users] soft-core and coulomb transformation

[Berk Hess]

Hi,

I am afraid you might be right.

I thought I had fixed all checks when implementing free energy for PME.
But it seems that the splines are only constructed for particles with 
non-zero

A charges.
If this is the (only) problem, it can easily be checked by replacing
in pme.c in spread_on_grid both lines:
if (!bHaveSplines) {
by
if (TRUE) {

If this is the problem, I will fix it, but then (probably) still retaining
the optimization of using the B-splines only once.

I guess normally one would choose the B-state to be the zero state.
But for mutation studies this bug (if it is really the problem) could
give small errors that one might not notice directly...

Berk.



From: "David Mobley" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users 
To: "bharat v. adkar" <[EMAIL PROTECTED]>
CC: Discussion list for GROMACS users 
Subject: Re: [gmx-users] soft-core and coulomb transformation
Date: Mon, 12 Nov 2007 08:45:33 -0800

Hi, Bharat, and David vdS.

This indeed is looking suspiciously like a real problem. FWIW, I did
reproduce your original problem using my own input files and PME with
gromacs 3.3.1.

It's still a bit perplexing, in that you seem to be getting basically
the "right" answers for the forward transformation (at least, by
comparing the PME forward results with the cutoff forward results) but
the reverse transformation is crazily wrong. I'm having a hard time
figuring out what sort of bug could cause this to happen.

The only thing I can come up with so far that might cause this is a
bug in the handling of B state 1-4 interactions with PME. Since
methane has no B state 1-4 electrostatic interactions, the
ethane->methane transformation would be OK both with and without PME.
But methane->ethane would go awry with PME because ethane still has
1-4 electrostatic interactions.

If I remember correctly, though, you reported that the vacuum
calculations work fine? That wouldn't be consistent with my
explanation above, and perhaps would suggest that the problem is
interactions with water, somehow?

Just speculation at this point.

I'm doing some more testing on this end (trying to come up with a more
minimal example). I'm checking to see whether discharging phenol in
water gives the same results as charging phenol in water.

David


On 11/11/07, bharat v. adkar <[EMAIL PROTECTED]> wrote:
>
> Hi David,
>I am keeping the subject same so that it is helpful to track in
> future :)
>
>
> On Sat, 10 Nov 2007, David Mobley wrote:
> > Dear Bharat,
> >
> > OK, I went ahead and ran with your topologies using my own run
> > scripts. My runs haven't finished yet,  but looking at just
> >  values from equilibration,  I seem to be seeing roughly
> > the same trends you do. In particular:
> > (1) The forward simulation always gives dv/dlambda values that are
> > fairly close to -2 at each lambda
> > (2) The reverse simulation gives a range of  values at
> > different lambda values, and switches from positive to negative as
> > lambda increases.
> >
> > The integral of  in the forward case is NOT the negative
> > of the integral of  for the reverse case, which is what it
> > should be.
> >
> > Obviously, something is wrong here, and it doesn't seem to be your run
> > input files. I don't see anything obviously wrong with your topology
> > files, either -- as far as I can tell your charge groups are OK.
> >
> > My suggestion is to try to strip this down to a simpler case where it
> > will become more clear what the problem is. Maybe ethane->methane
> > rather than with the capping on the ends.  (Did you say you have the
> > same problem with ethane->methane? It would be easier to troubleshoot
> > those topologies).
>
> As I mentioned earlier, ethane to methane transformation also shows the
> same behaviour. I am almost sure that the topologies and other input
> files are correct. I am pasting below the output of the
> coulomb-transformation for both, ethane to methane (forward) and methane
> to ethane (reverse). Topology is the same as i mentioned few mails
> back...
>
> Forward charge transformation
> lmbd  dg/dlerror
> 0.00 -8.286304 0.0108319
> 0.05 -8.32708  0.0114018
> 0.10 -8.328157 0.0095819
> 0.15 -8.344236 0.00893341
> 0.25 -8.353463 0.00984712
> 0.40 -8.368163 0.0104302
> 0.50 -8.397035 0.00969758
> 0.60 -8.415603 0.00908416
> 0.75 -8.448185 0.00941215
> 0.85 -8.484247 0.00922024
> 0.90 -8.481465 0.00885981
> 0.95 -8.495802 0.00961897
> 1.00 -8.501283 0.00957299
>
> Reverse charge transformation
> 0.00 13.770658 0.074592
> 0.05 13.331217 0.0778554
> 0.10 13.075527 0.0722786
> 0.15 12.483814 0.0750718
> 0.25 11.789282 0.0674654
> 0.40 10.730386 0.0875609
> 0.50 10.008684 0.0807128
> 0.60  9.266026 0.0736956
> 0.75  7.999017 0.0738001
> 0.85  7.388243 0.0832792
> 0.90  6.991334 0.0828869
> 0.95  6.595921 0.0796503
> 1.00  6.180366 0.0893983
>
> As can be clearly seen, both transformations are not equivalent. (These
> are output from the 1 ns simulations.)
>
>
> >
> > If you get to the point

RE: [gmx-users] force=nan in frame 0

[dongsheng zhang]

Dear Mark,

The installation works for other systems. The error happens in either EM or
MD. When I turn off all interaction potentials, the forces between all
particles should be zero, shouldn't they? Could you please tell me why the
initial forces are NaN? Thanks!

All the best!

Dongsheng

-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Mark Abraham
Sent: Sunday, November 11, 2007 9:04 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] force=nan in frame 0


dongsheng zhang wrote:
> Dear Mark,
> 
> Thank you for your reply. I have used gromacs before. In fact, I have 
> built this FF before, and using it successfully. My old computer was 
> crashed, so I need to do it again. The potential energies looked fine 
> in the md.log. Even I turn off all potentials. I still get the initial 
> foce = nan. Could you please give me any suggest about it?

Can't tell. You still haven't told us what you were trying to do when it 
crashed. EM, MD? Did you minimize and/or equilibrate? Does this 
installation run other systems?

Mark
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Re: [gmx-users] soft-core and coulomb transformation

[David Mobley]

Hi, Bharat, and David vdS.

This indeed is looking suspiciously like a real problem. FWIW, I did
reproduce your original problem using my own input files and PME with
gromacs 3.3.1.

It's still a bit perplexing, in that you seem to be getting basically
the "right" answers for the forward transformation (at least, by
comparing the PME forward results with the cutoff forward results) but
the reverse transformation is crazily wrong. I'm having a hard time
figuring out what sort of bug could cause this to happen.

The only thing I can come up with so far that might cause this is a
bug in the handling of B state 1-4 interactions with PME. Since
methane has no B state 1-4 electrostatic interactions, the
ethane->methane transformation would be OK both with and without PME.
But methane->ethane would go awry with PME because ethane still has
1-4 electrostatic interactions.

If I remember correctly, though, you reported that the vacuum
calculations work fine? That wouldn't be consistent with my
explanation above, and perhaps would suggest that the problem is
interactions with water, somehow?

Just speculation at this point.

I'm doing some more testing on this end (trying to come up with a more
minimal example). I'm checking to see whether discharging phenol in
water gives the same results as charging phenol in water.

David


On 11/11/07, bharat v. adkar <[EMAIL PROTECTED]> wrote:
>
> Hi David,
>I am keeping the subject same so that it is helpful to track in
> future :)
>
>
> On Sat, 10 Nov 2007, David Mobley wrote:
> > Dear Bharat,
> >
> > OK, I went ahead and ran with your topologies using my own run
> > scripts. My runs haven't finished yet,  but looking at just
> >  values from equilibration,  I seem to be seeing roughly
> > the same trends you do. In particular:
> > (1) The forward simulation always gives dv/dlambda values that are
> > fairly close to -2 at each lambda
> > (2) The reverse simulation gives a range of  values at
> > different lambda values, and switches from positive to negative as
> > lambda increases.
> >
> > The integral of  in the forward case is NOT the negative
> > of the integral of  for the reverse case, which is what it
> > should be.
> >
> > Obviously, something is wrong here, and it doesn't seem to be your run
> > input files. I don't see anything obviously wrong with your topology
> > files, either -- as far as I can tell your charge groups are OK.
> >
> > My suggestion is to try to strip this down to a simpler case where it
> > will become more clear what the problem is. Maybe ethane->methane
> > rather than with the capping on the ends.  (Did you say you have the
> > same problem with ethane->methane? It would be easier to troubleshoot
> > those topologies).
>
> As I mentioned earlier, ethane to methane transformation also shows the
> same behaviour. I am almost sure that the topologies and other input
> files are correct. I am pasting below the output of the
> coulomb-transformation for both, ethane to methane (forward) and methane
> to ethane (reverse). Topology is the same as i mentioned few mails
> back...
>
> Forward charge transformation
> lmbd  dg/dlerror
> 0.00 -8.286304 0.0108319
> 0.05 -8.32708  0.0114018
> 0.10 -8.328157 0.0095819
> 0.15 -8.344236 0.00893341
> 0.25 -8.353463 0.00984712
> 0.40 -8.368163 0.0104302
> 0.50 -8.397035 0.00969758
> 0.60 -8.415603 0.00908416
> 0.75 -8.448185 0.00941215
> 0.85 -8.484247 0.00922024
> 0.90 -8.481465 0.00885981
> 0.95 -8.495802 0.00961897
> 1.00 -8.501283 0.00957299
>
> Reverse charge transformation
> 0.00 13.770658 0.074592
> 0.05 13.331217 0.0778554
> 0.10 13.075527 0.0722786
> 0.15 12.483814 0.0750718
> 0.25 11.789282 0.0674654
> 0.40 10.730386 0.0875609
> 0.50 10.008684 0.0807128
> 0.60  9.266026 0.0736956
> 0.75  7.999017 0.0738001
> 0.85  7.388243 0.0832792
> 0.90  6.991334 0.0828869
> 0.95  6.595921 0.0796503
> 1.00  6.180366 0.0893983
>
> As can be clearly seen, both transformations are not equivalent. (These
> are output from the 1 ns simulations.)
>
>
> >
> > If you get to the point where you're convinced it has nothing to do
> > with your topology, you could submit a bugzilla -- but it would be a
> > good idea to be more sure that there is no problem with your topology,
> > first. Also it would be helpful to have more evidence about where the
> > bug might be, if there is one (hence the importance of stripping this
> > down to the "minimum" topology necessary to reproduce the problem).
> >
> > You might also, for example, just try turning off the charges on
> > methane in water. You could also try turning on the charges in methane
> > in water. These two should be equivalent (except for the sign) of
> > course.
> >
> > Keep me posted on what you find out.
>
> to further see what happens, i used cut-off instead of pme and that seems
> to be giving okay results. i tried running only 20 ps runs as in
> equilibration, and there the values look as per expectations. then tried
> with Ace-Ala-Nac <-> Ace-Gly-Nac also

[gmx-users] (no subject)

[pragya chohan]

hi.
Has anyone used inflategro provided on 
"http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis";. I am having 
problem in using it. When I enter my gro file no lipids are removed. Please 
reply.
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RE: [gmx-users] Tools for axial symmetry

[Henry O Ify]

stop mailing me please

Berk Hess <[EMAIL PROTECTED]> wrote:  
Exactly the tools you mention do work:
g_rdf has the option -xy
trjorder does not assume anything about the geometry
and will work fine in your case.

Berk.


>From: "Eudes Fileti" 
>Reply-To: Discussion list for GROMACS users 
>To: gmx-users@gromacs.org
>Subject: [gmx-users] Tools for axial symmetry
>Date: Mon, 12 Nov 2007 10:59:54 -0200
>
>Dear colleagues
>I have made simulation of infinite nanotubes in solvent environment.
>However I can not use the usual tools of the GROMACS to analyze my
>simulation
>(as g_rdf, trajorder, etc) due to axial symmetry (cylindrical).
>
>Problem that I need to solve are the calculation of rdf
>(taking as reference the axis of the nanotube, not the COM)
>and also the analysis of the number of molecules into the first solvation
>shell.
>
>Have anybody some suggestion of standalone program or GROMACS tools for 
>help
>me?
>
>Thanks
>eef
>--
>___
>Eudes Eterno Fileti
>Centro de Ciência Naturais e Humanas
>Universidade Federal do ABC
>Rua Catequese, 242 - 3º Andar
>09090-400 Santo André - SP Brasil
>Tel: +55 11 4437-1600 ramal 408
>skype: eefileti
>http://cromo.ufabc.edu.br/~fileti/


>___
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RE: [gmx-users] Tools for axial symmetry

[Berk Hess]

Exactly the tools you mention do work:
g_rdf has the option -xy
trjorder does not assume anything about the geometry
and will work fine in your case.

Berk.



From: "Eudes Fileti" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users 
To: gmx-users@gromacs.org
Subject: [gmx-users] Tools for axial symmetry
Date: Mon, 12 Nov 2007 10:59:54 -0200

Dear colleagues
I have made simulation of infinite nanotubes in solvent environment.
However I can not use the usual tools of the GROMACS to analyze my
simulation
(as g_rdf, trajorder, etc) due to axial symmetry (cylindrical).

Problem that I need to solve are the calculation of rdf
(taking as reference the axis of the nanotube, not the COM)
and also the analysis of the number of molecules into the first solvation
shell.

Have anybody some suggestion of standalone program or GROMACS tools for 
help

me?

Thanks
eef
--
___
Eudes Eterno Fileti
Centro de Ciência Naturais e Humanas
Universidade Federal do ABC
Rua Catequese, 242 - 3º Andar
09090-400  Santo André - SP Brasil
Tel: +55 11 4437-1600 ramal 408
skype: eefileti
http://cromo.ufabc.edu.br/~fileti/




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[gmx-users] Tools for axial symmetry

[Eudes Fileti]

Dear colleagues
I have made simulation of infinite nanotubes in solvent environment.
However I can not use the usual tools of the GROMACS to analyze my
simulation
(as g_rdf, trajorder, etc) due to axial symmetry (cylindrical).

Problem that I need to solve are the calculation of rdf
(taking as reference the axis of the nanotube, not the COM)
and also the analysis of the number of molecules into the first solvation
shell.

Have anybody some suggestion of standalone program or GROMACS tools for help
me?

Thanks
eef
-- 
___
Eudes Eterno Fileti
Centro de Ciência Naturais e Humanas
Universidade Federal do ABC
Rua Catequese, 242 - 3º Andar
09090-400  Santo André - SP Brasil
Tel: +55 11 4437-1600 ramal 408
skype: eefileti
http://cromo.ufabc.edu.br/~fileti/
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RE: [gmx-users] widom in Gromacs

[Berk Hess]

From: Argyrios Karatrantos <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users 
To: gmx-users@gromacs.org
Subject: [gmx-users] widom in Gromacs
Date: Mon, 12 Nov 2007 02:00:42 -0800 (PST)

Hi all,
  is it feasible to implement the widom method in Gromacs in a system
 of Lennard-Jones chains,
in other words to insert a molecule chain and calculate the
 difference of DeltaU=U(N+1)-U(N) ?
if it is feasible how this can be implemented

thanks all of you

regards


Gromacs 3.3 can insert single atoms.
Gromacs 4.0 will be able to insert molecules, including random rotation.

But when you say chain, it sounds like you want to insert something
quite big. This will never be feasible with Widom test particle insertion.

Berk.

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[gmx-users] widom in Gromacs

[Argyrios Karatrantos]

Hi all,
  is it feasible to implement the widom method in Gromacs in a system
 of Lennard-Jones chains,
in other words to insert a molecule chain and calculate the
 difference of DeltaU=U(N+1)-U(N) ?
if it is feasible how this can be implemented

thanks all of you

regards


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